4E4X

Crystal Structure of B-Raf Kinase Domain in Complex with a Dihydropyrido[2,3-d]pyrimidinone-based Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4E4X/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-03-13 Released: 2012-05-09 
• Deposition Author(s): Voegtli, W.C., Sturgis, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.315 
• R-Value Work: 0.273 
• R-Value Observed: 0.275 

Literature

The discovery of potent and selective pyridopyrimidin-7-one based inhibitors of B-Raf(V600E) kinase.

Ren, L., Ahrendt, K.A., Grina, J., Laird, E.R., Buckmelter, A.J., Hansen, J.D., Newhouse, B., Moreno, D., Wenglowsky, S., Dinkel, V., Gloor, S.L., Hastings, G., Rana, S., Rasor, K., Risom, T., Sturgis, H.L., Voegtli, W.C., Mathieu, S.

(2012) Bioorg Med Chem Lett 22: 3387-3391

• PubMed: 22534450 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.015
• Primary Citation of Related Structures:  
  4E4X


• PubMed Abstract: 
  

  Herein we describe the discovery of a novel series of ATP competitive B-Raf inhibitors via structure based drug design (SBDD). These pyridopyrimidin-7-one based inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. Optimization led to the identification of compound 17, a potent, selective and orally available agent with excellent pharmacokinetic properties and robust tumor growth inhibition in xenograft studies.

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Organizational Affiliation: 

Array BioPharma, Inc., 3200 Walnut Street, Boulder, CO 80301, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.37 kDa 
• Atom Count: 4,396 
• Modelled Residue Count: 541 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	307	Homo sapiens	Mutation(s): 0  Gene Names: BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens) Explore P15056  Go to UniProtKB:  P15056
PHAROS:  P15056 GTEx:  ENSG00000157764

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T1Q	C [auth A], D [auth B]	N-(2,4-difluoro-3-{2-[(3-hydroxypropyl)amino]-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl}phenyl)propane-1-sulfonamide C20 H23 F2 N5 O4 S HCWAUGCXCGOSNN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
T1Q	BindingDB:  4E4X	IC50: min: 7, max: 41 (nM) from 2 assay(s)
	PDBBind:  4E4X	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.315 
• R-Value Work: 0.273 
• R-Value Observed: 0.275 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109	α = 90
b = 109	β = 90
c = 155.21	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Voegtli, W.C., Sturgis, H.L.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations